应该是收集了水稻所有的ChIP-seq数据的一个网站Plants
2018-11-01 本文已影响18人
热衷组培的二货潜
首页界面
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看看更新频率，你没看错，前几天才更新。。
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随便拿一个基因输入看看（注意这里只支持RAPDB-ID）:Os11g0559200
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首先是这样的
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选择右边的tracks(分析的人都知道，这一班就意味着各种data),分八个板块
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比如我们想看组蛋白H3K27me3修饰，理所当然快捷选择antibody
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然后我这里选择看了水稻野生型DJ里面12天叶片的H3K27me3修饰
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可以看到这个基因上几乎没有H3K27me3修饰
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特别Nice的是还可以支持导入自己的数据，像bw、gff文件等。
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其次特别Nice的是给了所有分析脚本
分析命令
$ ./fastq-dump -I SRRxxxxx (for single-end sequencing)
$ ./fastq-dump -I --split-files SRRxxxxx (for pair-end sequencing)
- 使用软件版本以及质量过滤说明
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Reads qualities were analyzed with FastQC (v0.10.1) and the low quality bases (less than 30) were ignored in the following mapping step.
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All the raw reads were mapped to corresponding genomes with Bowtie2 (v2.3.4) and compressed to binary files using samtools (v1.7).
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比对到基因组
$ bowtie2 -5 xx -3 xx -x /directory/tair10 -U file.fastq -S file.sam
- Here, xx representsthe the position of the base will be trimmed from the reads before mapping. -5 and -3 indicates the direction of trimming (5’ end and 3’end, respectively); -x and tair10 indicate the mapping index. The index has to be built before mapping. Please see detail in bowtie2 manual.
将sam文件转换成bam文件
$ samtools view -bS file.sam > file.bam
$ samtools sort -T file -o file_sort.bam file.bam
$ samtools index file_sort.bam
- Finally, the mapped reads were converted to bigwig format for visualization by using bamcoverage (deeptools2) with the following settings: binsize 10, normalizing with 1x genome content (RPGC, Arabidopsis thaliana, 135,000,000; Glycine max, 978,000,000; Oryza sativa, 375,000,000; Zea mays, 2,135,000,000), ignorDuplicates, samFlagExclude 1796 and 1924 for single and pair-end sequencing, respectively. The following command will convert single-end Arabidopsis thaliana sorted bam file to bigwig file.
$ bamCoverage -b flie_sort.bam -o file_sort.bw -bs 10 --effectiveGenomeSize 135000000 --normalizeUsing RPGC --ignoreDuplicates -e 100 --samFlagExclude 1796
2.1.3 Generating peak plateau, FRiP, and median enrichment
- The following shell and three R scripts are used for generating figures of peak plateau, FRiP, and median enrichment from mapped binary file (bam file). A list of file name needs to be provided before running the script. All the files including scripts, bam files, and listshould be in the same directory.
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脚本内容
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Before running the script, several tools need to be installed and added to your executable path.
